PO Paper Winter 2011

Plans for a publication- TIPS paper

-This is a priority for the fall to promote the application of "Ontologies for Plant Sciences"

First manuscript will target journal: 'Trends in Plant science' for a Review/Opinion article.

-Laurel and Ramona will prepare a summary preproposal to be sent to Trends in Plant Science for their consideration.

Review/Opinion article pre-submission enquiries: provide a 500-600 word summary outlining

• what will be discussed in the article,
• why the suggested topic would be timely,

co-author information, plus up to 20 key references that indicate the intended breadth of the proposed article (most references should be to work published in the past 2-3 years).

Focus will be on the benefits and usefulness of the PO and GO, global perspective, links between PO and GO

-two papers to consider when writing this He et al, 2009 and Vincent et al, 2003

Topics/goals to include:

• What the PO is and types of data available on PO (background information), use info from the grant proposal

• Overall goals of the PO - take from grant introduction, screen shots of browser

• PO-based annotation can be used to improve analysis

• How to improve the analysis aspect of genomics using ontology-based annotation of expression and phenotypes

• Engage community, encourage folks to provide more annotations

Examples/use cases, (maybe for box?):

Compare gene expression data sets from Arabidopsis and rice: find common datasets- one each for a tissue and and growth stage

Sources: from Genevestigator

Also: Wang et al, 2010

Questions to ask:

-In the PO we currently have a large # of annotations to Arabidopsis (~532,000, from TAIR and NASC)

eg. Look at annotations to flower and compare to the data set from Qifa Zhang paper, covers ~15 tissues

What are the genes that are over or under expressed in each set? Annotate those genes based on that,

Then go back to data set from arab and how many genes expressed in flower from arab overlap with gene ontology.

Genevesitgator –Look for common data sets for rice and arab?

How many dots (genes or GO categories) connect these two data sets?

Laurel will work on coming up with an enriched data set (list of genes and expression profile).

Potential uses of PO

-interspecies comparison using Genevestigator

-hot topics in plant genomics and how the PO can help research in those areas

--e.g., rice data sets described above, new genomes being sequenced

-systematics (character descriptions), see Teleost Anatomy Ontology paper.

-evolutionary studies of homology and convergence, evo-devo, GO-type analyses

-crop improvement for non-model species (trait descriptions and gene expression as in SGN or Generation Challenge Program, gene exploration for non-model species based on model organism database in PO)

Actual use cases

-Virtual Plant

-GCP

-SGN

-Traitnet

-others?

Recruiting more contributors

-use the article as a way to get encourage contribution of annotations from more groups

Lol- find list of datasets and their descriptions- Genevestigator

• Introduce to the group on Friday afternoon

• work through list and confer with Pankaj- go over draft version- Sat am?

Possible citations (up to 20)

Gene Expression Atlasin rice (Zhang)

Krom and Ramakrishna 2008, Plant Phys

Lang et al. 2008 Exploring plant biodiversity: the Physcomitrella genome and beyond. TIPS

Rensing et al. 2008 The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science

Papanov et al. 2009 The evolution of nuclear auxin signalling. BMC Evolutionary Biology

Perez-Rodriguez et al. 2010 PInTFDB: updated content and new features of the plant transcription factor database. Nucleic Acids Research

van der Graaf et al. 2009 The WUS homeobox-containing (WOX) protein family. Genome Biology

Wolf et al. 2010 The Molecular and Physiological Responses of Physcomitrella patens to Ultraviolet-B Radiation. Plant Physiology

Bhasi et al. 2010 RoBuST: an integrated genomics resource for the root and bulb crop families Apiaceae and Alliaceae. Bmc Plant Biology

Plant Phys paper

Intro, results, methods:

Update on the changes to PO in the past 18 months, focus on how it is now applicable to all plants.

Challenges in incorporating such a phylogenetically broad group of species

-Compare to previous publication Ilic et al, Plant Phys.

Discussion:

how this will help move research forward in non-angiosperm model species and all non-model species

future directions

Second manuscript will be a full paper to Plant Physiology- Bioinformatics section, target date after the new year, once we complete more revisions.

Ideas from PJ Apple-Pseudo fruit, microarray data,

florets in rice and compositae. Compare large scale sequencing data sets.

-We have been keeping track of the changes on the 'Summary of Changes' page

Look at Qifa Zhang rice datasets see microarry data Gene Expression Atlas